The invention relates generally to detecting diseases of the urinary tract. Furthermore, the invention also relates to reagents and methods for detecting diseases of the urinary tract. More particularly, the present invention relates to reagents such as polynucleotide sequences and the polypeptide sequences encoded thereby, as well as methods which utilize these sequences. The polynucleotide and polypeptide sequences are useful for detecting, diagnosing, staging, monitoring, prognosticating, in vivo imaging, preventing or treating, or determining predisposition to diseases or conditions of the urinary tract such as urinary tract cancers.
The organs of the urinary tract include the bladder, kidneys, and ureter. The incidence of urinary tract cancers in the United States is projected to be 86,300 cases diagnosed and 24,700 related deaths to occur during 1998. The most prevalent of the urinary tract cancers is bladder cancer, with projections of 54,400 new cases diagnosed and 12,500 related deaths to occur during 1998 (American Cancer Society statistics). Bladder tumors are heterogeneous in their ability to progress and are characterized by a high rate of recurrence. Hence, bladder cancer patients are monitored closely following their initial treatment.
Diseases such as bladder cancer traditionally have been diagnosed by appearance of blood in urine (hematuria) and confirmed by more detailed visualization of cells in biopsy samples under a microscope by highly trained personnel. The standard surveillance technique to detect recurrent bladder cancer is cystoscopy. Flexible cystoscopes have made cystoscopy more acceptable to patients but the method remains invasive. Efforts to replace cystoscopy by examining voided urine for tumor cells have included cytopathology and flow cytometry but the sensitivities are not high enough to detect the majority of recurrence, particularly those that are well or moderately differentiated. Cost also limits their use as adjuncts to cystoscopy. Other urinary markers that might be useful for diagnosing recurrences are being developed, including nonspecific markers, such as various growth factors, immune complexes and tumor-related proteins. However, to date, no single test has proved reliable enough to gain widespread acceptance. In particular, no test to date has sufficient simplicity, sensitivity, specificity and cost effectiveness to warrant pre-symptomatic screening.
Following is a more detailed summary of methods and markers in urine that have been used for detection of bladder tumors, and their limitations: Hematuria is found in up to 20% of a target population (Mariani A J, Mariani M C, Macchioni C, Stams U K, Hariharan A, Moriera A. J Urol 141:350-355, 1989; Messing E M, Young T B, Hunt V B, Roecker E B, Vailiancourt A M, Hisgen W J, Greenberg E B, Kuglitsch M E, Wegenke, J D: J Urol 148:289-292, 1992; and Britton J P, Dowell A C, Whelan P, Harris C M. J Urol 148:788-790, 1992), and 4-9% of those will have malignancy. In one of the most recent studies, the BTA (basement membrane complexes) test showed sensitivity of 40%, 96% specificity for healthy volunteers and 80-90% specificity for patients with non-malignant genitourinary disease (Sarosdy M F, deVere White R W, Soloway M S, Sheinfeld J, Hudson M A, Schelihammer P F, Jarowenko M V, Adams G, Blumenstein B A: J Urol 154:379-384, 1995). Urinary basement membrane antigens have been found higher in invasive cancer, with sensitivity 58% and specificity 96% (Abou Farha K M M, Janknegt R A, Kester A D M, Arendt J W: Urol Int 50 133-140, 1993). The Aura-Tek FDP dipstick showed 69% sensitivity with a patient population and 96% specificity with a healthy population (Schmetter B S, Habicht K K, Lamm D L, Morales A, Grossman H B, Bander N, Hanna M G, Butman BR : J Urol 155:492A, 1996). Nuclear matrix protein NMP22 showed considerable overlap between patients with tumors and benign urological conditions (Carpinita G A, Stadler W M, Briggman J V, Chodak G W, Church P A, Lamm D L, Lange P H, Messing E M, Pasciak R M, Reservitz G B, Ross R N, Rukstalis D B, Sarosday M F, Soloway M S, Thiel R P, Vogelzang N, Hayden C L: J Urol 156:1280-1285, 1996). Carcinoembryonic antigen (CEA) has been shown to occur in urine of some patients with bladder cancer, but the potential diagnostic utility is unclear (Wahren B, Edsmyr F: Urol Res 6:221-224, 1978). High levels of autocrine motility factor (AMF) have been detected in urine of patients with bladder cancer, showing correlation with stage and grade, but the clinical utility has not been established (Guirguis R, Schiffman E, Liu B, Birbeck D, Engel J, Liotta L: J Nat Cancer Inst 80:1203-1211, 1988). Similarly, high levels of fibroblast growth factors (FGF) have been found in urine of some bladder cancer patients (O'Brien T S, Smith K, Cranston D, Fuggle S, Bicknell R, Harods A L: Brit J Urol 76:311-314, 1995; Nguyen M, Watanabe H, Budson E, Richie J P, Folkman J: J Nat Cancer Inst 85:241-242, 1993; Chopin D K, Caruelle J-P, Colmbel M, Pallcy S, Ravery V, Caruelle D, Abbout C C, Bardtault D: J Urol 160:1126-1130, 1991). Further, high urinary levels of Scatter Factor/Hepatocyte Growth Factor (SF/HGF) have been reported in patients with bladder cancer, but the data is as yet unconfirmed (Joseph A, Weiss G H, Lin L, Fuchs A, Chowdhury S, O'Shaugnessy P, Goldbert I D, Rosen E M: J Nat Cancer Inst 87:372-377, 1995). In one unconfirmed report, urinary type IV collagenase has been found to be higher in urine from patients with invasive cancers (Margulies I M K, Hoyhtya M, Evans C, Stracke M L, Liotaa L A, Stetler-Stevenson W G: Cancer Epidemiol Biomarkers Prev 1:467-474, 1992). Hyaluronic acid has recently been proposed as a 93% specific and 92% sensitive marker (Lokeshwar V B, Obeck C, Soloway M S, Block N L: Cancer res 57, 774-777, 1997), but the data remains to be confirmed by larger studies. Patent application EP 0678744A2 describes a urinary tumor associated protein which is characterized by being immunogenic in cancer patients. The antigen was not characterized in detail, and is unlikely to be a member of the keratin/cytokeratin family, since these are not known to be immunogenic in cancer patients. There is thus a great effort to discover specific urinary markers, but none have become routinely established.
Assays for urinary tumor markers based on proteins of the keratin/cytokeratin family have been described. Some of these assays use uncharacterized antibodies while others use antibodies with defined specificity. As suggested below, the basis of these assays appears to be selective release of soluble peptide fragments by tumorous cells. Furthermore, the literature suggests that keratins and cytokeratins are characteristic of the differentiated state of cells, and, where present, are indicative of the normal cellular origin of the tumor, not of the state of de-differentiation. Indeed, Nagle [Cancer & Metastasis Rev. 15:473-482 (1996)] states that intermediate filaments in general, including the cytokeratins as a class, are valuable markers for distinguishing the cellular origin of various undifferentiated neoplasms.
Sundstrom and Stigbrand (International Journal of Biological markers, 9, 102-108, 1994) state that cytokeratin markers are characteristic of the expression patterns of normal epithelial cells and the retention of the pattern is a useful means for classifying tumors. These authors also describe Tissue Polypeptide Antigen (TPA) as a complex of cytokeratins 8, 18 and 19. Carbin, Eckman and Eneroth (Urol Res 17, 269-272, 1989) state that TPA in serum and urine is the result of increased turnover and autolysis of malignant cells. Because of the poly-specificity of the TPA assays, any selectivity due to de novo synthesis would not be apparent, and, should only be detectable with specificity using probes or antibodies to epitopes which are unique for the specific keratin/cytokeratins which are up-regulated in the cancerous tissue. U.S. Pat. No. 533,832 describes a monoclonal antibody with reactivity to cytokeratins 8, 18 and 19, which they suggest might be useful for diagnosing cancer. There is no discussion of up-regulated proteins indicative of bladder cancer.
Attempts have been made to improve the specificity of assays by using TPA in combination with other markers (Halim A B, El-Amahdy O, Hamza S, Aboul-Ela M, Oehr P: International Journal of Biological markers, 7, 234-239, 1992; Casetta G, Piana P, Cavallini A, Vottero M, Tizzani A: Brit J Urol 72, 60-64, 1993). The specificity is still inadequate since false positives due to urinary tract infections may occur. Further, a diagnostic test based on a single marker is preferable to an assay using three markers. There have also been attempts to improve the TPA assay by the use of monoclonal antibodies (Sundstrom B E, d'Amico Y, Brundell J: Int J Biol Markers, 10, 166-173, 1995). However, these monoclonal antibodies were used only in an attempto mimic the oligo-specificity of the polyclonal antibody assay, and not to improve the specificity by looking at specific peptides up-regulated in the cancerous tissue.
Keratin 18 has been proposed for use as a target in more specific assays (Baker W C, White R D, Rossito P V, Min B H, Cardiff R D: J Urol 140, 436-439, 1988). However, the monoclonal antibodies used had cross-reactivity with keratin 8 (Rossito P V, Chan R, Strand M A, Miller C H, Baker W C, Deitsch A D, Devere White R, Cardiff R D: J Urol 140, 431-435, 1988). Furthermore, limited sensitivity and specificity was noted. Patent application PCT 95/31728 describes specific epitopes characteristic of cytokeratin 18 and detectable amounts of these epitopes in the serum of bladder cancer patients. However, the utility using these specific epitopes may be limited because of the specificity of the epitopes described. Further there is no suggestion of a general approach to look for keratins/cytokeratins up-regulated in bladder tumors. A commercial kit is available for cytokeratin 19, under the name Cyfra 21-1. With that kit, problems occur due to the occurrence of cells and cell debris in urine which must be first removed in order to determine soluble fragments (Dittado R, Bariolli P, Gion M, Mione R, Barichello M, Capitanio G, Cocco G, Cazzolato G, de Biasi F, Praturlon F, Antinozzi R, Gianneo E: Clin Chem 42, 1634-1638, 1996). False positives were obtained in patients with cystitis (Senga Y, Kimura G, Hattori T, Yoshida K: Urology 48, 703-710, 1996). None of the above works determined the merits of markers which are specifically up-regulated in bladder tumors. In a comprehensive study, Moll et al (Moll R, Achtstatter T, Balcarova-Stander J, Ittensohn M and Franke WW: Amer J Pathol 132, 123-144, 1988) showed that cytokeratins 7, 8, 13, 19 are present in normal urothelium, and that 13 was greatly reduced in grade three transitional cell carcinoma. No mention was made of any species being present in increased amounts in the cancer.
Brinkman et al (Proc Natl Acad Sci USA 1995 October 24;92(22): 10427-10431) have discovered a gene referred to as CAS (cellular apoptosis susceptibility). They have also observed that this gene is amplified and has increased expression in certain tumorous cell lines from leukemia, colon and breast cancer (Genome Res 1996 March; 6(3): 187-194). See, also, PCT Publication No. WO 9640713.
Morrison et al (Oncogene 1994, vol 9 pp 3417-3426, Journal of Biological Chemistry, vol 270, pp 2176-2182) have described a class of proteins which are expressed in tumors initiated by the oncogene neu but absent from those initiated by c-myc. One of these, a chloride channel protein, mat-8, was proposed as having diagnostic utility for breast cancer (PCT application WO96/05322).
However, to date, there has been no suggestion for using the above proteins as diagnostic markers for urinary tract diseases.